TRIUMPH Microbial Genomics course: Glossary

Key Points

Welcome
Introduction	Sequencing E.coli isolates to determine assocations of bacterial genes with antibiotic resistance
Sequence Read Quality Lecture	Determining sequence quality of reads
Sequence assembly	Assembly is a process which aligns and merges fragments from a longer DNA sequence in order to reconstruct the original sequence. Assembly is a time consuming process. Make sure you plan it well
Introduction day 2	Discussing issues from day 1
Sequence Assembly Lecture	Assembly is a process which aligns and merges fragments from a longer DNA sequence in order to reconstruct the original sequence. Quality can be assessed using N50 but also using other methods
Sequence Quality	Quality of a genome assembly can be assessed by looking at some basic statistics on the assembly, but also by using an external reference
Self Study: Inspecting sequence graphs	A genome assembly can be fragmented because of repeats in the genome. The assembly graph display possible connections between contigs.
MLST	Multi Locus Sequence Typing can be used to track strains MLST resolution is not very high but it is still useful Sequence errors can lead to incomplete MLST types
Resistance genes	Resistance genes can be found on the chromosome and on plasmids Point mutations are often in essential chromosomal genes The translation from resistance genotype to phenotype is not always easy
Introduction day 3 - work on day 2 exercises by yourself	Discussing issues from day 2 and catching up
Plasmid typing and classification	Resistance genes can be found on the chromosome and on plasmids Plasmid classification by hand is time consuming. Especially with lots of contig, automated analysis is better There are also plasmids without resistance genes
Annotation	Genome annotation includes prediction of protein-coding genes, as well as other functional genome units It often starts by identifying open reading frames Predicted sequences are further analysed with BLAST Larger DNA sequences or genomes require automated prediction and annotation
Visualizing genomic regions using Clinker	Resistance genes can be found on the chromosome and on plasmids Visualizing the region can help understand the history of the genetic locus containing the resistance gene
Introduction day 4	Discussing issues from day 3 and catching up
Pangenome analysis	The microbial pangenome is the union of genes in genomes of interest. The microbial core genome is the intersection of genes shared by genomes of interest. Roary is a pipeline to determine genes of the pangenome.
Phylogenetic trees from the core genome and visualization	A tree can be generated from a combined set of genes for better resolution. More genes = more resolution
Self Study: Bacterial GWAS Lecture	GWAS is the association of genes, snps, kmers with phenotypes observed Population structure is needed to correct for linkage disequilibrium Multiple testing correction is needed to deal with false positives
Self Study: Bacterial GWAS	Contigency testing for gene presence absence to associate a genotype with a phenotype, similar to GWAS in clinical genetics is possible with bacterial genomes
Wrapup	Colistin resistance is associated with mcr-1

Glossary

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